7RRK: Fluorescent protein Dronpa

Name: PDB 7RRK: Crystal structure of fast switching M159E mutant of fluorescent protein Dronpa (Dronpa2)
Published: 2021-10-13
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: fluorescent protein

Crystal structure of fast switching M159E mutant of fluorescent protein Dronpa (Dronpa2). Determined by X-ray diffraction at 1.93 Å resolution. Released 13 Oct 2021.

Method: X-ray diffraction
Resolution: 1.93 Å
Organism: Echinophyllia sp. SC22
Chains: 8
Atoms: 15,363
Mol. weight: 231.92 kDa
Released: 13 Oct 2021

Explore 7RRK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7RRK contains 49 α-helices and 108 β-strands across 8 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains A, B, C, D and F: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	1
β-strand	21-32	12	1
β-strand	37-46	10	1
α-helix	48	1
α-helix	50	1
α-helix	55-58	4
β-strand	70	1	1
α-helix	78-81	4
β-strand	87-95	9	1
β-strand	100-110	11	1
β-strand	113-123	11	1
β-strand	136-139	4	1
α-helix	140-141	2
β-strand	142-149	8	1
β-strand	152-163	12	1
β-strand	168-179	12	1
α-helix	184-187	4
β-strand	189-200	12	1
β-strand	206-216	11	1

Chain E: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	5
β-strand	21-32	12	5
β-strand	37-46	10	5
α-helix	48	1
α-helix	50	1
α-helix	54-56	3
β-strand	70	1	5
α-helix	78-81	4
β-strand	87-95	9	5
β-strand	100-110	11	5
β-strand	113-123	11	5
α-helix	130-133	4
β-strand	136-139	4	5
α-helix	140-141	2
β-strand	142-149	8	5
β-strand	152-163	12	5
β-strand	168-179	12	5
α-helix	184-187	4
β-strand	189-200	12	5
β-strand	206-216	11	5

Chains G and H: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	7
β-strand	21-32	12	7
β-strand	37-46	10	7
α-helix	48	1
α-helix	50	1
α-helix	55-58	4
β-strand	70	1	7
α-helix	78-81	4
β-strand	87-95	9	7
β-strand	100-110	11	7
β-strand	113-123	11	7
β-strand	136-139	4	7
α-helix	140-141	2
β-strand	142-149	8	7
β-strand	152-163	12	7
β-strand	164	1	8
β-strand	166	1	8
β-strand	168-179	12	7
α-helix	184-187	4
β-strand	189-200	12	7
β-strand	206-216	11	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fluorescent protein Dronpa	A, B, C, D, E, F, G, H	protein	255	Echinophyllia sp. SC22	Q5TLG6 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H), FASTA

>7RRK_1 Fluorescent protein Dronpa (chains A, B, C, D, E, F, G, H)
GSSHHHHHHSSGLVPGGSHMVSKGEENNMAVIKPDMKIKLRMEGAVNGHPFAIEGVGLGK
PFEGKQSMDLKVKEGGPLPFAYDILTTVFXNRVFAKYPENIVDYFKQSFPEGYSWERSMN
YEDGGICNATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWEPSTEKLYVRDGVLK
GDVNEALSLEGGGHYRCDFKTTYKAKKVVQLPDYHFVDHHIEIKSHDKDYSNVNLHEHAE
AHSGLPRQAMDELYK

Primary citation

Energetic Basis and Design of Enzyme Function Demonstrated Using GFP, an Excited-State Enzyme. Lin, C.Y., Romei, M.G., Mathews, I.I. et al. J Am Chem Soc (2022) 144:3968-3978. DOI 10.1021/jacs.1c12305 · PubMed

Other PDB entries of the same protein (UniProt Q5TLG6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2IE2 1.7 Å, The 1.7 A crystal structure of Dronpa: a photoswitchable green fluorescent protein
7RRH 1.75 Å, Crystal structure of fast switching R66M/M159T mutant of fluorescent protein Dronpa…
2Z1O 1.75 Å, Crystal structure of a photoswitchable GFP-like protein Dronpa in the bright-state
2GX2 1.8 Å, Crystal structural and functional analysis of GFP-like fluorescent protein Dronpa
2IOV 1.8 Å, Bright-state structure of the reversibly switchable fluorescent protein Dronpa
2Z6Z 1.8 Å, Crystal structure of a photoswitchable GFP-like protein Dronpa in the bright-state
5HZU 1.89 Å, Crystal structure of Dronpa-Ni2+
6MYB 1.9 Å, Room-temperature structure of deuterated Tetdron (isomorph 1)
2GX0 1.9 Å, Crystal structural and functional analysis of GFP-like fluorescent protein
2POX 1.95 Å, Dark state structure of the reversibly switchable fluorescent protein Dronpa
4EMQ 1.95 Å, Crystal structure of a single mutant of Dronpa, the green-on-state PDM1-4
4HQ8 1.95 Å, Crystal structure of a green-to-red photoconvertible DRONPA, pcDRONPA in the…

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